After more than 10 years of treatments against water pollution, the water quality of the Huaihe River has improved considerably. At present, the river is in recovery phase. Two surveys on macro-invertebrates were carried out in the middle reaches in May and October 2010. Fifteen sampling stations were set up along the trunk, including Hongze Lake. Thirty-four species were recorded, and poor species and low biodiversity were the main community characteristics of this river. Significant differences in assemblages were found between the trunk and lake. Collectors were the chief functional feeding group in the trunk, while predators were the chief group in the lake. The species number in Hongze Lake decreased considerably compared to the historical data. Total phosphorus and temperature were important factors affecting the distribution of macroinvertebrates in the trunk, while pH, dissolved oxygen, and chlorophyll were the important factors in the lake. Sand mining, industrial and non-point pollution, and urbanization were the important factors causing degradation of whole aquatic ecosystems in the river basin. Two new alien species from the Yangtze River were first recorded in Hongze Lake, and the previous recorded alien species Nephthys sp. has spread into the whole lake and the trunk. Due to having similar histories of water pollution, the Huaihe would experience a process of recovery similar to the Rhine River.